Genomic and phylogeographical analysis revealed CTX-M-55 producing Escherichia coli ST10 and ST2325 clones of One Health concern from dairy farm waste in Gansu, China

Abstract

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli resists broad-spectrum cephalosporins, considered as a critical priority pathogen, and its presence in animals, humans, and the environment highlights its significance as a One Health issue. Dairy farm waste is a potential environmental contaminant and can serves as a significant reservoir for the emergence and spread of ESBL-producing E. coli, which belongs to One Health clones and poses a serious global threat. This study aimed to investigate the occurrence and genomic characteristics of ESBL-producing E. coli clones of One Health concern from dairy farm waste in Gansu, China. In this study, we isolated and characterized two CTX-M-55 ESBL-producing E. coli strains, ZYX8158 and ZYS8091, which belong to One Health clones. The genomic analysis revealed a large resistome, mobilome, virulome, and plasmidome was acquired by both ESBL-producing E. coli strains. The genome-based typing revealed that E. coli ZYX8158 and ZYS8091 belonged to globally disseminated clones ST10 (O73:H31 serotype) and ST2325 (O66:H25 serotype), respectively. Phylogeographical analysis revealed both strains as potential One Health clones due to their clustering with related E. coli strains isolated from animal, human, and environmental sources, regardless of geographical boundaries, indicating their zoonotic potential and clonal spread in the One Health sector. This study highlights that dairy farm waste can be a potential source of the emergence and dissemination of One Health clones of critical priority ESBL-producing E. coli in One Health settings, which demands continuous and integrated genomic surveillance for comprehensive knowledge and mitigation strategies.

Keywords: ESBL-producing E. coli; Genomic surveillance; Mobilome; One Health clones; Resistome; Virulome.

Fig. 1

Phylogenetic analysis based on core-genome SNPs and distribution of virulence factors (VFs) and serotypes of the present study E. coli strains and their comparison with verified E. coli pathotypes. AT = autotransporter, SP = siderophore. EAEC, Enteroaggregative E. coli; AIEC, Adherent-invasive E. coli; UPEC, Uropathogenic E. coli; APEC, avian pathogenic E. coli; NMEC, Neonatal meningitis E. coli; EHEC, Enterohemorrhagic E. coli; STEC, Shiga toxin-producing E. coli; ETEC, Enterotoxigenic E. coli.

Fig. 2

The phylogenetic tree of geographically closely related clones based on core-genome MLST allelic profiles (Table S2, Table S3). (A) The phylogeographical analysis of ESBL-producing E. coli ST10 (ZYX8158) and closely related isolates. Our study revealed E. coli ST10 clones circulating across France, the USA, Australia, China, the United Kingdom, South Korea, Germany, Mexico, Canada, Tanzania, Ireland, and Ecuador (Retrieved data in Table S2). (B) The phylogeographical analysis of ESBL-producing E. coli ST2325 (ZYS8091) and closely related isolates. Our study revealed that ST2325 clones have been identified in the USA, the United Kingdom, Germany, China, and Pakistan (Retrieved data in Table S3). The phylogenetic tree of geographically closely related clones based on core-genome MLST allelic profiles (Tables S2 and S3). (A) The phylogeographical analysis of ESBL-producing E. coli ST10 (ZYX8158) and closely related isolates. Our study revealed E. coli ST10 clones circulating across France, the USA, Australia, China, the United Kingdom, South Korea, Germany, Mexico, Canada, Tanzania, Ireland, and Ecuador (Retrieved data in Table S2). (B) The phylogeographical analysis of ESBL-producing E. coli ST2325 (ZYS8091) and closely related isolates. Our study revealed that ST2325 clones have been identified in the USA, the United Kingdom, Germany, China, and Pakistan (Retrieved data in Table S3).